miaViz

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see miaViz.

Microbiome Analysis Plotting and Visualization


Bioconductor version: 3.14

The miaViz package implements plotting function to work with TreeSummarizedExperiment and related objects in a context of microbiome analysis. Among others this includes plotting tree, graph and microbiome series data. The package is part of the broader miaverse framework.

Author: Felix G.M. Ernst [aut, cre] , Tuomas Borman [aut] , Leo Lahti [aut]

Maintainer: Felix G.M. Ernst <felix.gm.ernst at outlook.com>

Citation (from within R, enter citation("miaViz")):

Installation

To install this package, start R (version "4.1") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("miaViz")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("miaViz")
miaViz HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Microbiome, Software, Visualization
Version 1.2.1
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License Artistic-2.0 | file LICENSE
Depends R (>= 4.0), SummarizedExperiment, TreeSummarizedExperiment, mia(>= 0.99), ggplot2, ggraph (>= 2.0)
Imports methods, stats, S4Vectors, BiocGenerics, BiocParallel, DelayedArray, scater, ggtree, ggnewscale, viridis, tibble, tidytree, tidygraph, rlang, purrr, tidyr, dplyr, ape, DirichletMultinomial
System Requirements
URL
See More
Suggests knitr, rmarkdown, BiocStyle, testthat, patchwork, microbiomeDataSets
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package miaViz_1.2.1.tar.gz
Windows Binary miaViz_1.2.1.zip (32- & 64-bit)
macOS 10.13 (High Sierra) miaViz_1.2.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/miaViz
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/miaViz
Bioc Package Browser https://code.bioconductor.org/browse/miaViz/
Package Short Url https://bioconductor.org/packages/miaViz/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive